R Notebook

Patterns were learned on the 6mo MENs and the gut cell atlas was projected into them. Now look at the subset of non-fetal healthy samples and visualize the pattern usages

library(monocle3)
library(dplyr)
library(here)

source(here("scripts/accessory_functions/monocle_mods.R"))
source(here("scripts/accessory_functions/pattern_plotting.R"))

obj_fn <- "/data/users/jared/atlas_processing/gut_cell_atlas/data/mesenchymal_gut_nonfetal_healthy.Rds"

cds <- readRDS(obj_fn)

Pattern definitions in 6month LMMP

knitr::include_graphics(here("plots/NMF/lmmp/old_pattern_run/50dims/LMMP_pattern_feature_correlation.pdf"))

cell_wt <- data.table::fread(here("teichman_gut_atlas/data/gut_atlas_in_6mo_LMMP_old_patterns.csv"), data.table = F)
colnames(cell_wt)[1] <- "cell_index"

all(colnames(cds) %in% rownames(cell_wt))

[1] FALSE

From previously generated pattern projections, load in values and merge with existing pData

pData(cds) <- pData(cds) %>%
  as.data.frame() %>%
  tibble::rownames_to_column(var = "cell_index") %>%
  left_join(., cell_wt, by = "cell_index") %>%
  tibble::column_to_rownames(var = "cell_index") %>%
  DataFrame

plot_cells_mod(cds, color_cells_by = "Age") + facet_wrap(~ Age)

No trajectory to plot. Has learn_graph() been called yet?

Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

plot_cells_mod(cds, color_cells_by = "Integrated_05", label_cell_groups = F) +
  theme(legend.position = "none") +
  facet_wrap(~ Integrated_05)

No trajectory to plot. Has learn_graph() been called yet?

npatt <- 50
lapply(1:npatt, plotCellPatterns, cds, do.clip = c(0.01,0.99))

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

No trajectory to plot. Has learn_graph() been called yet?

Cells aren't colored in a way that allows them to be grouped.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

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